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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcctctgtagagacaaaatctctctcttgctcagtccttcacctcaccctcgtggcctcgctctccctcacacattgttgtacctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCTATTCTGATTGACCAG

Basic information

species Oryza sativa
transcript LOC_Os01g71300.2
intron # 4
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|313081136|gb|HO213722.1|HO213722
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGGAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|33793936|gb|CF322856.1|CF322856
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88252124|gb|CI350552.1|CI350552
EST:     GGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGGTGCAACAAAATTTCAACTCC
genomic: GGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAA-GTGCAACAAAATTTCAACTCC
EST: gi|86522305|gb|CI162511.1|CI162511
EST:     TAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: TAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|58678471|gb|CK067158.1|CK067158
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88201956|gb|CI202311.1|CI202311
EST:     AAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: AAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|29616411|gb|CB621423.1|CB621423
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGGAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88215812|gb|CI215661.1|CI215661
EST:     ATCAGATTGGAAG                         GAATATAATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: ATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88837009|gb|CI008445.1|CI008445
EST:     AATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: AATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88213104|gb|CI212768.1|CI212768
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|89166731|gb|CI104017.1|CI104017
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|163921069|gb|EG710132.1|EG710132
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|86513942|gb|CI156575.1|CI156575
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88201927|gb|CI202282.1|CI202282
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|58601416|gb|CK011944.1|CK011944
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|218484537|gb|FG954358.1|FG954358
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88977256|gb|CI024993.1|CI024993
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88205446|gb|CI205295.1|CI205295
EST:     TCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: TCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|86252680|gb|CI010162.1|CI010162
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|86884561|gb|CI337129.1|CI337129
EST:     TCAGATTGGAAG                         GAATATGATCCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: TCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88958572|gb|CI096088.1|CI096088
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|2443065|gb|C74836.1|C74836
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|86594394|gb|CI251266.1|CI251266
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|86490058|gb|CI132691.1|CI132691
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAGTCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|87032354|gb|CI264135.1|CI264135
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88202985|gb|CI202834.1|CI202834
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|33793279|gb|CF322520.1|CF322520
EST:     GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|86496146|gb|CI138779.1|CI138779
EST:     GCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
EST: gi|88967655|gb|CI016170.1|CI016170
EST:     GTCAGAAAGCATTCTCCAACTATTTGGGCCCAGCTAAATCAGATTGGAAG                         GAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT
genomic: GTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAGgtaattcctc ... ctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacctcaccctcgtggcctcgctctccctcacacattgttgtacctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCTATTCTGATTGACCAG
                                           acctaac  putative branch site (score: 2)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcctctgtagagacaaaatctctctcttgctcagtccttcacctcaccctcgtggcctcgctctccctcacacattgttgtacctaactgcagGAATATGATGCAACCTGCCTGATCAAGAAGTGCAACAAAATTTCAACTCCTATTCTGATTGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT